Using the GUI.

Open the target image in Fiji, and browse to the CSV file from the GUI. It will be parsed and the parameter lists will be populated with the headers of the CSV file. Some columns are mandatory (X, Y, frame). If you uncheck Compute all features? box, only a minimal set of features will be declared and computed.

Depending on whether you specify to import the track values or not, the TrackMate GUI will be created at a different stage.

Running the exporter from the command line.

After installation, a Jython script called CsvToTrackMate.py will be addede to the scripts folder of your Fiji installation. It is meant to be called in [[Headless|headless mode]] to directly convert a CSV file and an image file into a TrackMate file.

You can use Fiji in headless mode, to call the Jython script CsvToTrackMate.py that will parse arguments and configure the importer properly. Here is an example: